| PairwiseAlignedXStringSet-class {Biostrings} | R Documentation |
The PairwiseAlignedXStringSet class is a container for storing an
elementwise pairwise alignment.
The PairwiseAlignedFixedSubject class is a container for storing a
pairwise alignment with a single subject.
The PairwiseAlignedFixedSubjectSummary class is a container for storing
the summary of an alignment.
## Constructors:
## When subject is missing, pattern must be of length 2
## S4 method for signature 'XString, XString':
PairwiseAlignedXStringSet(pattern, subject,
type = "global", substitutionMatrix = NULL, gapOpening = 0, gapExtension = -1)
## S4 method for signature 'XStringSet, missing':
PairwiseAlignedXStringSet(pattern, subject,
type = "global", substitutionMatrix = NULL, gapOpening = 0, gapExtension = -1)
## S4 method for signature 'character, character':
PairwiseAlignedXStringSet(pattern, subject,
type = "global", substitutionMatrix = NULL, gapOpening = 0, gapExtension = -1,
baseClass = "BString")
## S4 method for signature 'character, missing':
PairwiseAlignedXStringSet(pattern, subject,
type = "global", substitutionMatrix = NULL, gapOpening = 0, gapExtension = -1,
baseClass = "BString")
pattern |
a character vector of length 1 or 2, an XString,
or an XStringSet object of length 1 or 2. |
subject |
a character vector of length 1 or an XString object. |
type |
type of alignment. One of "global", "local",
"overlap", "global-local", and "local-global" where
"global" = align whole strings with end gap penalties,
"local" = align string fragments,
"overlap" = align whole strings without end gap penalties,
"global-local" = align whole strings with end gap penalties on
pattern and without end gap penalties on subject.
"local-global" = align whole strings without end gap penalties on
pattern and with end gap penalties on subject. |
substitutionMatrix |
substitution matrix for the alignment. If NULL, the diagonal values and off-diagonal values are set to 0 and 1 respectively. |
gapOpening |
the cost for opening a gap in the alignment. |
gapExtension |
the incremental cost incurred along the length of the gap in the alignment. |
baseClass |
the base XString class to use in the alignment. |
Before we define the notion of alignment, we introduce the notion of "filled-with-gaps subsequence". A "filled-with-gaps subsequence" of a string string1 is obtained by inserting 0 or any number of gaps in a subsequence of s1. For example L-A–ND and A–N-D are "filled-with-gaps subsequences" of LAND. An alignment between two strings string1 and string2 results in two strings (align1 and align2) that have the same length and are "filled-with-gaps subsequences" of string1 and string2.
For example, this is an alignment between LAND and LEAVES:
L-A
LEA
An alignment can be seen as a compact representation of one set of basic operations that transforms string1 into align1. There are 3 different kinds of basic operations: "insertions" (gaps in align1), "deletions" (gaps in align2), "replacements". The above alignment represents the following basic operations:
insert E at pos 2
insert V at pos 4
insert E at pos 5
replace by S at pos 6 (N is replaced by S)
delete at pos 7 (D is deleted)
Note that "insert X at pos i" means that all letters at a position >= i
are moved 1 place to the right before X is actually inserted.
There are many possible alignments between two given strings string1 and string2 and a common problem is to find the one (or those ones) with the highest score, i.e. with the lower total cost in terms of basic operations.
In the code snippets below,
x is a PairwiseAlignedXStringSet object, except otherwise noted.
pattern(x):
The AlignedXStringSet object for the pattern.
subject(x):
The AlignedXStringSet object for the subject.
summary(object, ...):
Generates a summary for the PairwiseAlignedXStringSet.
In the code snippets below,
x is a PairwiseAlignedXStringSet object, except otherwise noted.
alphabet(x):
Equivalent to alphabet(unaligned(subject(x))).
length(x):
The length of the aligned(pattern(x)) and aligned(subject(x)).
There is a method for PairwiseAlignedFixedSubjectSummary as well.
type(x):
The type of the alignment ("global", "local",
"overlap", "global-local", or "local-global").
There is a method for PairwiseAlignedFixedSubjectSummary as well.
In the code snippets below,
x is a PairwiseAlignedFixedSubject object, except otherwise noted.
aligned(x, degap = FALSE, gapCode="-", endgapCode="-"):
If degap = FALSE, ``align" the alignments by returning an
XStringSet object containing the aligned patterns without
insertions. If degap = TRUE, returns
aligned(pattern(x), degap=TRUE).
The gapCode and endgapCode arguments denote the code in the
appropriate alphabet to use for the internal and end gaps.
as.character(x):
Converts aligned(x) to a character vector.
as.matrix(x):
Returns an "exploded" character matrix representation of aligned(x).
toString(x):
Equivalent to toString(as.character(x)).
In the code snippets below,
x is a PairwiseAlignedFixedSubject object, except otherwise noted.
consensusMatrix(x, baseOnly=FALSE, freq=FALSE, gapCode="-",
endgapCode="-")
See `consensusMatrix` for more information.
consensusString(x)
See `consensusString` for more information.
coverage(x, start=NA, end=NA, shift=0L, width=NULL, weight=1L)
See `coverage,PairwiseAlignedFixedSubject-method` for more
information.
Views(subject, start=NULL, end=NULL, width=NULL, names=NULL):
The XStringViews object that represents the pairwise alignments
along unaligned(subject(subject)). The start and end
arguments must be either NULL/NA or an integer vector
of length 1 that denotes the offset from start(subject(subject)).
In the code snippets below,
x is a PairwiseAlignedXStringSet object, except otherwise noted.
nchar(x):
The nchar of the aligned(pattern(x)) and aligned(subject(x)).
There is a method for PairwiseAlignedFixedSubjectSummary as well.
nindel(x):
An InDel object containing the number of insertions and deletions.
score(x):
The score of the alignment.
There is a method for PairwiseAlignedFixedSubjectSummary as well.
x[i]:
Returns a new PairwiseAlignedXStringSet object made of the selected
elements.
rep(x, times):
Returns a new PairwiseAlignedXStringSet object made of the repeated
elements.
P. Aboyoun
pairwiseAlignment,
AlignedXStringSet-class,
XString-class,
XStringViews-class,
align-utils,
pid
PairwiseAlignedXStringSet("-PA--W-HEAE", "HEAGAWGHE-E")
pattern <- AAStringSet(c("HLDNLKGTF", "HVDDMPNAL"))
subject <- AAString("SMDDTEKMSMKL")
nw1 <- pairwiseAlignment(pattern, subject, substitutionMatrix = "BLOSUM50",
gapOpening = -3, gapExtension = -1)
pattern(nw1)
subject(nw1)
aligned(nw1)
as.character(nw1)
as.matrix(nw1)
nchar(nw1)
score(nw1)
nw1